R3T46W last accessed: 2022-11-04

Other names: HGVD, Human Genetic Variation Repository

The Human Genetic Variation Database (HGVD) aims to provide a central resource to archive and display Japanese genetic variation and association between the variation and transcription level of genes. The database currently contains genetic variations determined by exome sequencing of 1,208 individuals and genotyping data of common variations obtained from a cohort of 3,248 individuals. The HGVD browser can be used to view allele and genotype frequencies, number of samples, coverages, and expression QTL (eQTL) significances.

Webpage:

http://www.hgvd.genome.med.kyoto-u.ac.jp/

Licence:

Name: HGVD Terms of Use
URL: http://www.hgvd.genome.med.kyoto-u.ac.jp/about.html

Publications:

Publications
More detailed information about this field from each metasource.

Human genetic variation database, a reference database of genetic variations in the Japanese population
PMID: 26911352
metasource: Fairsharing.org
version: None

Human genetic variation database, a reference database of genetic variations in the Japanese population PubMed citations: 126.

126 articles citing: Human genetic variation database, a reference database of genetic variations in the Japanese population

Genetic analysis of Japanese patients with small bowel adenocarcinoma using next-generation sequencing. PMID:35778698
Familial Hyperaldosteronism Type 3 with a Rapidly Growing Adrenal Tumor: An In Situ Aldosterone Imaging Study. PMID:35723389
Aberrant hypomethylation at imprinted differentially methylated regions is involved in biparental placental mesenchymal dysplasia. PMID:35581658
Rheumatoid arthritis in a patient with compound heterozygous variants in the COL11A2 gene and progressive hearing loss: A case report. PMID:35363175
Whole-exome sequencing in a Japanese multiplex family identifies new susceptibility genes for intracranial aneurysms. PMID:35299232
Pan-human consensus genome significantly improves the accuracy of RNA-seq analyses. PMID:35256454
Whole exome analysis of patients in Japan with hearing loss reveals high heterogeneity among responsible and novel candidate genes. PMID:35248088
Association between germline pathogenic variants and breast cancer risk in Japanese women: The HERPACC study. PMID:35218119
Amelioration of a neurodevelopmental disorder by carbamazepine in a case having a gain-of-function GRIA3 variant. PMID:35031858
Founder genetic variants of ABCC4 and ABCC11 in the Japanese population are not associated with the development of subacute myelo-optico-neuropathy (SMON). PMID:34951141
Retroperitoneal Paraganglioma With Asymptomatic Follicular Lymphoma: A Case Report. PMID:34877445
Heterozygous missense variant of the proteasome subunit β-type 9 causes neonatal-onset autoinflammation and immunodeficiency. PMID:34819510
A Novel Heterozygous Missense Variant in the CIAO1 Gene in a Family with Alzheimer's Disease: The Val67Ile Variant Promotes the Interaction of CIAO1 and Amyloid-β Protein Precursor. PMID:34569959
Progressive B cell depletion in human MALT1 deficiency. PMID:34559885
Genetic and epigenetic basis of hepatoblastoma diversity. PMID:34538872
Sweat-gland carcinoma with neuroendocrine differentiation (SCAND): a clinicopathologic study of 13 cases with genetic analysis. PMID:34518631
Examination of the predicted prevalence of Gitelman syndrome by ethnicity based on genome databases. PMID:34373523
Molecular classification of blood and bleeding disorder genes. PMID:34272389
Phenotypic recapitulation and correction of desmoglein-2-deficient cardiomyopathy using human-induced pluripotent stem cell-derived cardiomyocytes. PMID:33949662
How understudied populations have contributed to our understanding of Alzheimer's disease genetics. PMID:33889936
Substantial anti-gout effect conferred by common and rare dysfunctional variants of URAT1/SLC22A12. PMID:33821957
Targeted Double-Stranded cDNA Sequencing-Based Phase Analysis to Identify Compound Heterozygous Mutations and Differential Allelic Expression. PMID:33804940
Allele frequency of variants reported to cause adenine phosphoribosyltransferase deficiency. PMID:33707627
Genome wide association study of HTLV-1-associated myelopathy/tropical spastic paraparesis in the Japanese population. PMID:33649182
A unique missense variant in the E1A-binding protein P400 gene is implicated in schizophrenia by whole-exome sequencing and mutant mouse models. PMID:33602898
SPG9A with the new occurrence of an ALDH18A1 mutation in a CMT1A family with PMP22 duplication: case report. PMID:33573605
Chronic Hypercapnic Respiratory Failure in an Adult Patient with Silver-Russell Syndrome. PMID:33518558
A novel splice-site mutation of the HNF1B gene in a family with maturity onset diabetes of the young type 5 (MODY5). PMID:33434175
KCNV2-Associated Retinopathy: Genetics, Electrophysiology, and Clinical Course-KCNV2 Study Group Report 1. PMID:33309813
Comparative characterization of PCDH19 missense and truncating variants in PCDH19-related epilepsy. PMID:33262389
A novel mutation in the SLCO2A1 gene, encoding a prostaglandin transporter, induces chronic enteropathy. PMID:33166338
Premature aging syndrome showing random chromosome number instabilities with CDC20 mutation. PMID:33094908
Genetics of fulminant type 1 diabetes. PMID:33088637
RMVar: an updated database of functional variants involved in RNA modifications. PMID:33021671
Whole-exome sequencing of 79 xenografts as a potential approach for the identification of genetic variants associated with sensitivity to cytotoxic anticancer drugs. PMID:32986753
Human NINEIN polymorphism at codon 1111 is associated with the risk of colorectal cancer. PMID:32934817
Genetic Studies of Hypertrophic Cardiomyopathy in Singaporeans Identify Variants in TNNI3 and TNNT2 That Are Common in Chinese Patients. PMID:32815737
Determination of novel CYP2D6 haplotype using the targeted sequencing followed by the long-read sequencing and the functional characterization in the Japanese population. PMID:32759992
Novel mutation identified in Leber congenital amaurosis - a case report. PMID:32736544
Patient-derived ovarian cancer organoids capture the genomic profiles of primary tumours applicable for drug sensitivity and resistance testing. PMID:32724113
Chemosensitivity of Patient-Derived Cancer Stem Cells Identifies Colorectal Cancer Patients with Potential Benefit from FGFR Inhibitor Therapy. PMID:32708005
Prevalence of disease-causing genes in Japanese patients with BRCA1/2-wildtype hereditary breast and ovarian cancer syndrome. PMID:32566746
Consolidated BRCA1/2 Variant Interpretation by MH BRCA Correlates with Predicted PARP Inhibitor Efficacy Association by MH Guide. PMID:32486089
Prospective avenues for human population genomics and disease mapping in southern Africa. PMID:32440765
Clinical characterization of patients with leucine-rich repeat kinase 2 genetic variants in Japan. PMID:32398759
Association between rs1229984 in ADH1B and cancer prevalence in a Japanese population. PMID:32337031
Variants encoding a restricted carboxy-terminal domain of SLC12A2 cause hereditary hearing loss in humans. PMID:32294086
The benign c.344G > A: p.(Arg115His) variant in the LDLR gene interpreted from a pedigree-based genetic analysis of familial hypercholesterolemia. PMID:32252761
Genetic Spectrum of EYS-associated Retinal Disease in a Large Japanese Cohort: Identification of Disease-associated Variants with Relatively High Allele Frequency. PMID:32218477
VPS13D-related disorders presenting as a pure and complicated form of hereditary spastic paraplegia. PMID:31876103
Genome-wide association analyses identify two susceptibility loci for pachychoroid disease central serous chorioretinopathy. PMID:31872073
KAT6B-related disorder in a patient with a novel frameshift variant (c.3925dup). PMID:31871732
Japanese version of The Cancer Genome Atlas, JCGA, established using fresh frozen tumors obtained from 5143 cancer patients. PMID:31863614
Schaaf-Yang syndrome shows a Prader-Willi syndrome-like phenotype during infancy. PMID:31791363
Rare compound heterozygous missense SPATA7 variations and risk of schizophrenia; whole-exome sequencing in a consanguineous family with affected siblings, follow-up sequencing and a case-control study. PMID:31695380
A missense variant in PER2 is associated with delayed sleep-wake phase disorder in a Japanese population. PMID:31527662
Frequent retrotransposition of endogenous genes in ERCC2-deficient cells derived from a patient with xeroderma pigmentosum. PMID:31455402
Germline mismatch repair gene variants analyzed by universal sequencing in Japanese cancer patients. PMID:31386297
Entire FGF12 duplication by complex chromosomal rearrangements associated with West syndrome. PMID:31311986
Atypical Familial Amyotrophic Lateral Sclerosis with Slowly Progressing Lower Extremities-predominant Late-onset Muscular Weakness and Atrophy. PMID:31257275
Is the population of Sado Island genetically close to the population of western Japan? PMID:31231535
Nonsense mutation in CFAP43 causes normal-pressure hydrocephalus with ciliary abnormalities. PMID:31004071
Mutation analyses by next-generation sequencing and multiplex ligation-dependent probe amplification in Japanese autosomal dominant polycystic kidney disease patients. PMID:30989420
Germline-Derived Gain-of-Function Variants of Gsα-Coding GNAS Gene Identified in Nephrogenic Syndrome of Inappropriate Antidiuresis. PMID:30962325
Clinicopathological and Genetic Profiles of Cases with Myocytes Disarray-Investigation for Establishing the Autopsy Diagnostic Criteria for Hypertrophic Cardiomyopathy. PMID:30959811
The desmosome is a mesoscale lipid raft-like membrane domain. PMID:30943110
Pathogenetic basis of Takenouchi-Kosaki syndrome: Electron microscopy study using platelets in patients and functional studies in a Caenorhabditis elegans model. PMID:30872706
Temple syndrome in a patient with variably methylated CpGs at the primary MEG3/DLK1:IG-DMR and severely hypomethylated CpGs at the secondary MEG3:TSS-DMR. PMID:30846001
Genome-wide association meta-analysis of functional outcome after ischemic stroke. PMID:30796134
Impact of cardiac myosin light chain kinase gene mutation on development of dilated cardiomyopathy. PMID:30690923
Genetic basis for plasma amino acid concentrations based on absolute quantification: a genome-wide association study in the Japanese population. PMID:30659259
INDEX-db: The Indian Exome Reference Database (Phase I). PMID:30615482
Identification of a rare homozygous SZT2 variant due to uniparental disomy in a patient with a neurodevelopmental disorder. PMID:30560016
VarGenius executes cohort-level DNA-seq variant calling and annotation and allows to manage the resulting data through a PostgreSQL database. PMID:30541431
Phylogenetic and mutational analyses of human LEUTX, a homeobox gene implicated in embryogenesis. PMID:30479355
Evaluating Clinical Genome Sequence Analysis by Watson for Genomics. PMID:30474028
GATA4 variant identified by whole-exome sequencing in a Japanese family with atrial septal defect: Implications for male sex development. PMID:30455927
TIRAP p.R81C is a novel lymphoma risk variant which enhances cell proliferation via NF-κB mediated signaling in B-cells. PMID:30381301
The Medical Genome Reference Bank: a whole-genome data resource of 4000 healthy elderly individuals. Rationale and cohort design. PMID:30353151
Exome and copy number variation analyses of Mayer-Rokitansky-Küster- Hauser syndrome. PMID:30302266
PLA2G6-associated neurodegeneration presenting as a complicated form of hereditary spastic paraplegia. PMID:30302010
Tumorigenicity-associated characteristics of human iPS cell lines. PMID:30286143
Clinical and genetic backgrounds of hypertrophic cardiomyopathy with mid-ventricular obstruction. PMID:30206291
Independent occurrence of de novo HSPD1 and HIP1 variants in brothers with different neurological disorders - leukodystrophy and autism. PMID:30083362
Regional genetic differences among Japanese populations and performance of genotype imputation using whole-genome reference panel of the Tohoku Medical Megabank Project. PMID:30041597
GCH1 mutations in dopa-responsive dystonia and Parkinson's disease. PMID:29948246
Genetic background of Japanese patients with pediatric hypertrophic and restrictive cardiomyopathy. PMID:29907873
Phosphorylation of the RSRSP stretch is critical for splicing regulation by RNA-Binding Motif Protein 20 (RBM20) through nuclear localization. PMID:29895960
Development of a molecular diagnostic test for Retinitis Pigmentosa in the Japanese population. PMID:29785639
Genomic analysis identifies masqueraders of full-term cerebral palsy. PMID:29761117
An unclassified variant of CHD7 activates a cryptic splice site in a patient with CHARGE syndrome. PMID:29531775
Multiancestry genome-wide association study of 520,000 subjects identifies 32 loci associated with stroke and stroke subtypes. PMID:29531354
A Novel p.L145Q Mutation in the HNF1B Gene in a Case of Maturity-onset Diabetes of the Young Type 5 (MODY5). PMID:29491316
A homozygous NOP14 variant is likely to cause recurrent pregnancy loss. PMID:29440706
Whole-exome sequencing and gene-based rare variant association tests suggest that PLA2G4E might be a risk gene for panic disorder. PMID:29391400
Novel and recurrent RNF213 variants in Japanese pediatric patients with moyamoya disease. PMID:29387438
Risk estimation model for nonalcoholic fatty liver disease in the Japanese using multiple genetic markers. PMID:29385134
A genome-wide association study in the Japanese population identifies the 12q24 locus for habitual coffee consumption: The J-MICC Study. PMID:29367735
Novel therapeutic strategy for cervical cancer harboring FGFR3-TACC3 fusions. PMID:29358619
Genome-wide association study of self-reported food reactions in Japanese identifies shrimp and peach specific loci in the HLA-DR/DQ gene region. PMID:29348432
Clinical features of chronic enteropathy associated with SLCO2A1 gene: a new entity clinically distinct from Crohn's disease. PMID:29313109
Whole exome sequencing to identify genetic markers for trastuzumab-induced cardiotoxicity. PMID:29247589
Identification of MYLK3 mutations in familial dilated cardiomyopathy. PMID:29235529
Evaluation of reported pathogenic variants and their frequencies in a Japanese population based on a whole-genome reference panel of 2049 individuals. PMID:29192238
Phenotypic expression of a novel desmin gene mutation: hypertrophic cardiomyopathy followed by systemic myopathy. PMID:29167554
DBTSS/DBKERO for integrated analysis of transcriptional regulation. PMID:29126224
MGST2 and WNT2 are candidate genes for comitant strabismus susceptibility in Japanese patients. PMID:29062608
Delineating SPTAN1 associated phenotypes: from isolated epilepsy to encephalopathy with progressive brain atrophy. PMID:29050398
Population Stratification in Genetic Association Studies. PMID:29044472
Integrated molecular analysis of Tamoxifen-resistant invasive lobular breast cancer cells identifies MAPK and GRM/mGluR signaling as therapeutic vulnerabilities. PMID:28935545
Mutation status of RAD51C, PALB2 and BRIP1 in 100 Japanese familial breast cancer cases without BRCA1 and BRCA2 mutations. PMID:28796317
Deep sequencing reveals variations in somatic cell mosaic mutations between monozygotic twins with discordant psychiatric disease. PMID:28765789
Hypoxia-Sensitive COMMD1 Integrates Signaling and Cellular Metabolism in Human Macrophages and Suppresses Osteoclastogenesis. PMID:28723554
Leveraging splice-affecting variant predictors and a minigene validation system to identify Mendelian disease-causing variants among exon-captured variants of uncertain significance. PMID:28714225
Korean Variant Archive (KOVA): a reference database of genetic variations in the Korean population. PMID:28655895
A novel PGK1 mutation associated with neurological dysfunction and the absence of episodes of hemolytic anemia or myoglobinuria. PMID:28580215
A burden of rare variants in BMPR2 and KCNK3 contributes to a risk of familial pulmonary arterial hypertension. PMID:28388887
Routine genetic testing of lung cancer specimens derived from surgery, bronchoscopy and fluid aspiration by next generation sequencing. PMID:28350094
Role of Structural Bioinformatics in Drug Discovery by Computational SNP Analysis: Analyzing Variation at the Protein Level. PMID:28302551
Rapid and cost-effective high-throughput sequencing for identification of germline mutations of BRCA1 and BRCA2. PMID:28179634
Biallelic Mutations in MYPN, Encoding Myopalladin, Are Associated with Childhood-Onset, Slowly Progressive Nemaline Myopathy. PMID:28017374
The Clinical Next-Generation Sequencing Database: A Tool for the Unified Management of Clinical Information and Genetic Variants to Accelerate Variant Pathogenicity Classification. PMID:28008688
KRIT1 mutations in three Japanese pedigrees with hereditary cavernous malformation. PMID:27766163
Germline Variants of Prostate Cancer in Japanese Families. PMID:27701467
A novel missense mutation of COL5A2 in a patient with Ehlers-Danlos syndrome. PMID:27656288
A Putative Association of a Single Nucleotide Polymorphism in GPR126 with Aggressive Periodontitis in a Japanese Population. PMID:27509131

Tags:

Tags
More detailed information about this field from each metasource.

gene
metasource: Fairsharing.org
version: None

genome
metasource: Fairsharing.org
version: None

genome visualization
metasource: Fairsharing.org
version: None

quantitative trait loci
metasource: Fairsharing.org
version: None

sequence variant
metasource: Fairsharing.org
version: None

transcript
metasource: Fairsharing.org
version: None

japanese
metasource: re3data.org
version: re3data.org: Human Genetic Variation Repository; editing status 2021-06-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3T46W last accessed: 2022-11-04

genetics
metasource: re3data.org
version: re3data.org: Human Genetic Variation Repository; editing status 2021-06-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3T46W last accessed: 2022-11-04

genomics
metasource: re3data.org
version: re3data.org: Human Genetic Variation Repository; editing status 2021-06-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3T46W last accessed: 2022-11-04

human
metasource: re3data.org
version: re3data.org: Human Genetic Variation Repository; editing status 2021-06-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3T46W last accessed: 2022-11-04

next-generation sequencers
metasource: re3data.org
version: re3data.org: Human Genetic Variation Repository; editing status 2021-06-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3T46W last accessed: 2022-11-04

pathogenic variations
metasource: re3data.org
version: re3data.org: Human Genetic Variation Repository; editing status 2021-06-16; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3T46W last accessed: 2022-11-04

gene genome genome visualization quantitative trait loci sequence variant transcript japanese genetics genomics human next-generation sequencers pathogenic variations

More to explore:

1/20

Previous Next

Need help integrating and/or managing biomedical data?

Webpage:

Licence:

Publications:

Publications
More detailed information about this field from each metasource.

Human genetic variation database, a reference database of genetic variations in the Japanese population
PMID: 26911352
metasource: Fairsharing.org
version: None

More to explore:

1/20

European Variation Archive

Pharmacogenomics Knowledge Base

GTEx

PhenoModifier

Chicken Variation Database

MutDB

Database of Single Nucleotide Polymorphism

The International Genome Sample Resource

Leiden Open Variation Database

SNPedia

BC SNPmax

Animal Quantitative Trait Loci (QTL) Database

ClinVar

CHDGKB

VnD

CanVaS

GWAS Central

Database of genomic structural VARiation

Genetic Epidemiology Simulation Database

Genome Variation Ontology

Webpage:

Licence:

Publications: Publications More detailed information about this field from each metasource. × Human genetic variation database, a reference database of genetic variations in the Japanese population PMID: 26911352 metasource: Fairsharing.org version: None Close

More to explore:

1/20

European Variation Archive

Pharmacogenomics Knowledge Base

GTEx

PhenoModifier

Chicken Variation Database

MutDB

Database of Single Nucleotide Polymorphism

The International Genome Sample Resource

Leiden Open Variation Database

SNPedia

BC SNPmax

Animal Quantitative Trait Loci (QTL) Database

ClinVar

CHDGKB

VnD

CanVaS

GWAS Central

Database of genomic structural VARiation

Genetic Epidemiology Simulation Database

Genome Variation Ontology

Publications:

Publications
More detailed information about this field from each metasource.

Human genetic variation database, a reference database of genetic variations in the Japanese population
PMID: 26911352
metasource: Fairsharing.org
version: None